TY - GEN
T1 - Joint base-calling of two DNA sequences with factor graphs
AU - Shi, Xiaomeng
AU - Lun, Desmond S.
AU - Meldrim, Jim
AU - Kötter, Ralf
AU - Médard, Muriel
PY - 2008
Y1 - 2008
N2 - To improve the utility of existing technologies based on Sanger sequencing, this paper examines the possibility of base-calling two superposed DNA sequences jointly. This approach allows a single electrophoresis experiment to process two sequences, using the same quantity of reagents and machine hours as for a single sequence. A practical heuristic is proposed to first estimate the peak parameters, then separate them into two sequences (major/minor) by passing messages on a factor graph. Base-calling on the major alone yields accuracy commensurate with single sequence approaches, and joint base-calling provides results for the minor which, while being of lesser quality, incurs no additional cost and can be ultimately used in the genome assembly process.
AB - To improve the utility of existing technologies based on Sanger sequencing, this paper examines the possibility of base-calling two superposed DNA sequences jointly. This approach allows a single electrophoresis experiment to process two sequences, using the same quantity of reagents and machine hours as for a single sequence. A practical heuristic is proposed to first estimate the peak parameters, then separate them into two sequences (major/minor) by passing messages on a factor graph. Base-calling on the major alone yields accuracy commensurate with single sequence approaches, and joint base-calling provides results for the minor which, while being of lesser quality, incurs no additional cost and can be ultimately used in the genome assembly process.
KW - DNA sequencing
KW - Factor graphs
UR - http://www.scopus.com/inward/record.url?scp=51449112552&partnerID=8YFLogxK
U2 - 10.1109/ICASSP.2008.4518043
DO - 10.1109/ICASSP.2008.4518043
M3 - Conference contribution
AN - SCOPUS:51449112552
SN - 1424414849
SN - 9781424414840
T3 - ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
SP - 2049
EP - 2052
BT - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
T2 - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
Y2 - 31 March 2008 through 4 April 2008
ER -